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BMCBI
2006
143views more  BMCBI 2006»
13 years 7 months ago
Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction
Background: One of the most powerful methods for the prediction of protein structure from sequence information alone is the iterative construction of profile-type models. Because ...
Eric D. Scheeff, Philip E. Bourne
NAR
2008
101views more  NAR 2008»
13 years 5 months ago
RNALogo: a new approach to display structural RNA alignment
Regulatory RNAs play essential roles in many essential biological processes, ranging from gene regulation to protein synthesis. This work presents a web-based tool, RNALogo, to cr...
Tzu-Hao Chang, Jorng-Tzong Horng, Hsien-Da Huang
BMCBI
2004
177views more  BMCBI 2004»
13 years 7 months ago
Gapped alignment of protein sequence motifs through Monte Carlo optimization of a hidden Markov model
Background: Certain protein families are highly conserved across distantly related organisms and belong to large and functionally diverse superfamilies. The patterns of conservati...
Andrew F. Neuwald, Jun S. Liu
BMCBI
2007
112views more  BMCBI 2007»
13 years 7 months ago
PFAAT version 2.0: A tool for editing, annotating, and analyzing multiple sequence alignments
Background: By virtue of their shared ancestry, homologous sequences are similar in their structure and function. Consequently, multiple sequence alignments are routinely used to ...
Daniel R. Caffrey, Paul H. Dana, Vidhya Mathur, Ma...
BMCBI
2007
156views more  BMCBI 2007»
13 years 7 months ago
Accuracy of structure-based sequence alignment of automatic methods
Background: Accurate sequence alignments are essential for homology searches and for building three-dimensional structural models of proteins. Since structure is better conserved ...
Changhoon Kim, Byungkook Lee